Have you tried under all surname variants on Griffith Valuation? Remember to check listings for North and South Ridings of Tipperary as well as Tipperary. As the girl on the ship was from Waterford, look at Waterford too. If she was the right one the family may have lived near the county boundary.
Another possibility is that Frances had left home and had been working in Waterford prior to emigration.
Your Frances' father being a labourer, he may have moved around for work, around Ireland or across to Britain. Convenient transport links between SE Ireland and Wales.
Tithe Applotment Books record only people who held titheable land. A labourer was unlikely to be included. None of my ancestors, small farmers, were in them; Tithe Applotment records for their townlands include very few entries compared to the number of people holding land there.
The Frances on the ship was stated to be C. of E. (Church of Ireland as she was Irish). Have you looked at "List of Church of Ireland Parish Registers"
https://www.ireland.anglican.org to see what survives for parishes in Tipperary and Waterford? Genealogy resources list can be found by selecting "About" tab. The Parish Registers list is in alphabetical order by parish name. Updated versions of the list are published so check publication date to ensure you're looking at latest. Some parishes may cross county boundaries. A diocese may include several counties. A county may be in more than 1 diocese.